Evangelion: Final Age of Reclamtion
by Hannible
Summary: More than five hundred years after third impact, Shinji awakens on Reach, after being cryogenically frozen, to find humanity recovering from a devastating war. A New war soon erupts as a stronger covenant with new goal in mind again attempts to light Halo
1. Chapter 1

**Prologue: Glass Desert, planet Reach March 29, 2558. Six years since the end of the covenant war. More than 500 years since third impact.**

" Sir, Noble team has arrived at the targets crash site." General Whitcomb looked on the over head display. " Tell the Colonel and his team to recon the area and look for possible hostiles. When they have confirmed the areas secure, I want them to move in closer to investigate." " Yes sir!" Said the young captain at the communications post, opening a channel to the colonel and relaying the orders.

Colonel Matt Garmin opened a link to the rest of his six man squad. " Fan out, check for possible hostiles and report back, Section three isn't taking any chances on this one understand?" Five green aknowdgment lights came on. Of course they understood, Garmin thought to him self, We're Spartans. In five minutes, five all clear signals were sent to the Colonel. " This is Spartan 445, area secured, awaiting further orders." The slightly static reply came " All right 445, move in a secure the object." " Understood Command."

Garmin opened a channel " All right, move in and secure the object." As Garmin moved forward his second in command Terry walked up to him. " Why did we get sent out on this one sir? This is waste of a Spartan deployment. ODST's would be better for this. Hell regulars would've done." " I don't know, and frankly, I don't give a Damn," replied Garmin. " Its not our job to ask questions, just think of it as a training session."

Garmin came over the impact craters lip " What the hell?" Terry came up to " Jesus!" He exclaimed " Just what the fuck is that thing?" Garmin opened a Channel to command. " Sir, we are at the crash site. You're not going to believe this. Linking helmet feed now." Back at the command center the fuzzy image of the commander helmet cam came up on the main viewer. Command was astonished, Before them sat a giant purple robot. " Command," Garmin's voice cackled through the speakers. " We have a survivor down here. Young male, Approximately 14 to 15 years old. His vitals are in bad shape, suggest you send a pelican with fully equipped med team." " Roger 445, pelican in bound , estimated arrival in 2 minutes."

Garmin stood over the boy, looking at him. Suddenly the boys opened and looked right at the Colonel. His eyes were a piercing cobalt blue. He raised his hand and tried to say something, but grimaced in paint before passing out again. His vitals suddenly dropped to near nothing. Garmin was about to perform first aid when the pelican arrived and the med teams took the aboard. The Colonel knew in that boys state, only one thing would save him. He hoped he was strong enough to endure it.

Garmin looked to his team as the pelican took off. " Radio for VTOL heavy lift gear. Lets get this thing back to base." The acknowledgement light blinked green.


	2. Augmentation

**Evangelion: Final Age of Reclamation Part one- Age of Discovery**

**Chapter one- Augmentation.**

Garmin looked down from a glass paneled observation room into the operating room. On the table covered by a white sheet and hooked up to life support systems was the young man he and his team had found in the Glass dessert. The automatic doors behind him opened. He didn't have to look to know who it was.

" How is he Doctor Halsey?" Garmin asked, still looking out the observation room. Halsey could his face reflected in the window, his face a hard expression on it, as though he already knew the answer to his own question.

" He is stable, but…" Halsey started.

" But what Doctor?"

Halsey gulped. She knew the Colonel wouldn't like this next part. Not one bit.

" Section three wants him for…Study." She said nervously. Every one knew about the Colonel and Section Three. Judging from his expression there was still bad blood there.

" Study my ass. All they want to do is cut him open and see what makes him tick. Bastards." Garmin said to him self. Halsey nodded agreeing. " It's wrong." She said.

" Catherine?" Garmin asked, Shocking Halsey with his use of her first name, " We can't let that happen. He doesn't deserve to die in a lab as some kind of expirment."

Though Halsey agreed, she saw no way out of the situation. Well there was one way, but Halsey had sworn shhe never again ruin someones life that way. She knew immediately from the look at on the colonels face what he was going to ask.

" No, I wont do it. I swore I'd never ruin someone that way again."

Garmin turned to look at her. " Its murder if we don't. I can read those instruments as well as you can Doctor. He is dying, Section three knows this and will hurry to make sure that they can get what they want. Regardless of the fact that he's human."

Halsey was torn. She hated what she had done to Garmin and those like him, it was one of her greatest regrets, but she also knew that if the young man on the table didn't undergo augmentation he would die. And as a Spartan, he would become to Valuable for section three to use that way.

" Why? Is there really no other way?" Halsey asked. Garmin just shook his head.

" Why me? Why not one of the other doctors?"

" Because Catherine, I trust you. Look, I know what I'm asking you is hard, but please. Catherine please help him if we don't he's dead, if we do, well he may still die but if he survies then he'll at least have a fighting chance." Garmin pleaded with her.

Halsey relented " Ok, I'll do it. I'll just make up reason that will look good to section three." Halsey said.

" Thank you Doctor." Garmin said. He turned and headed for the door, as it opened Halsey called to him.

" You miss her don't you?" She asked looking him in the eye. Garmin looked her right back " I don't know what your talking about." he said coldly, and exited the room. Garmin walked back to his quarters to lay down. Thinking the whole way back. He looked over at his desk as he entered his quarters. The only picture on it was of him and pretty blonde woman sitting near a tree smiling. Garmin picked it up, looking at it memories flashed through his mind bringing tears as he remembered all the good times he'd had with her. Garmin remembered the last time he'd seen her, before her assignment to section three. He has finally told her that he loved her, and found out she felt the same. Then two months after she left, she was killed in action. Garmin looked at the picture again, sobbing now and threw it against the wall shattering it. Yes, he did miss her. More than any one knew.

**Operating room.**

" Well. Lets get this over with." Said Halsey. She looked over to her assistant.

" Get ready to begin stage one." Her assistant nodded an hooked up the boy to several machines. The machines came to life whirring and humming. The status lights on the machine blinked red then green. The tech looked up at Halsey.

" Its all ready doctor." he said.

" Good begin stage one of the Augmentation process." The tech nodded and gave the activate command. Six needles extended and entered the boy along his spine and began to inject their serum into him. Even in his sedated state he was cringing in pain.

" Stage one of augmentation successfully initiated. His body is accepting the muscle enhancers." the tech reported.

"Good. Prepare stage Two." The tech nodded and began stage two. The six neddles withdrew from his spine and refilled with blue liquid, then re-inserted into his spine. Halsey watched the data on her screen. Muscle mass had appropriately risen and the adrenal stimulant was working perfectly. He was ready for stage three.

" Begin stage three. Put him on the HGH drip. By morning he'll be ready for the final stage of his augmentation." Halsey watched as the tech scurried around and did as he was asked. As they left the operating room, she looked back the boy sleeping uncomfortably on the table. " I'm sorry." She whispered.

**Restricted area 18. R&D hangar.**

The massive purple creature stood in the hangar bay as techs ran around underneath it. Inside the hangar stood six other beings like it, though these appeared to be wearing MOLJNER battle armor. They were labled units 10 through 16. Each was an Evangelion, now ready for activation. All they needed was some pilots.

A man sat at his desk in a non descript office just off of restricted area 18. His name plate said Director Haverson. He was the commander of Section three. On his desk were six files of Spartans. Each one was a potential pilot. Garmins folder was on the top of the list.

**Next day. Operating room.**

Halsey looked at the face of the young man nervously. This was the most dangerous part of the whole part of the process. She remembered the first time she had done this operation. How many had either died or were so maimed they would never again function normally. She took a deep breath calming herself and looked up at the observation room to see Garmin standing in his dress uniform. He nodded to her.

Halsey began the incisions. Cutting down the the young mans bones. Once she could see the bones, she injected the combination of Carbon fibers and metal alloys that would make his bones virtually unbreakable. This whole process took well into the afternoon. Soon she was finished and moved on to the final stage.

This was the tricky part. She had to open his skull and install a neural uplink that would allow the young man to control his MOLJNER battle armor and synch with an A.I.

Halsey had some concerns however, as this was the new uplink made by ONI. Colonel Garmin and six other Spartans were the only other ones with this next generation uplink. She was wondering as to why ONI wanted him to have this uplink as well, as the original trial size required was six and they already had that.

Halsey shook her head and cast those thoughts to the side. She'd find out why later. Halsey made her incision and began to gently insert the uplink. When she was finished she went to the control console near his bead. Hasley's finger hovered over the activate button. Once the uplink was on, there was no going back. She looked again to the Colonel in the observatory, he nodded and she pushed the button.

" I'm sorry." She whispered again to the young man.

**2 day later. Recovery room 232 C**

Shinji began to stir.

" Unfamiliar ceiling." he muttered. Shinji felt a dull ache threw out his body, what happened? He thought to himself. He remembered seeing Asuka torn to shreds by the MP EVA series, then a massive Rei and Kouru floating in the air. Things got a little fuzzy after that, then he saw earth the blue green shining orb he called home getting father and father away, then nothing but inky blackness.

" I see your awake." Said a voice in the corner. Shinji looked over toward the voice seeing a tall handsome looking man of only maybe 17 or 18 looking back at him. The man was massive. He stood about 7 feet tall and was well muscled. His eyes were cold and his face hard. He was wearing a Black T-shirt and Combat fatigues with a pistol strapped to his right thigh.

" What's your name?" asked the man.

" Shinji Ikari." Shinji responded

" Pleased to meet you, my name is Matthew Garmin. I am a Colonel in the UNSC armed forces and a Spartan combat soilder."

What the hell is this guy talking about? He wondered. This was really confusing. What is the UNSC?

" Where am I?" Shinji asked, he needed some answers.

" You are on Reach, Aproximatley 10.5 light years from earth."

That stament set off alarm bells in Shinji's mind. I'm not on earth?

" What's the date?" he asked, afraid of the answer.

" April 10th 2558." the man answered

Shinji passed out on the bed. " What did I say?" Garmin wondered, confused.

**Undisclosed location.**

" How are our plans coming along?" Asked a man

" Very well," replied another " the covenant has pledged their support to us, and the new Eva units will soon be ready for them."

" Excellent. Soon every thing will begin. We will end the UNSC , light the rings and bring forth Universal Instrumentality."

A/N: I redid this chapter because I wrote it at one am in the morning and when I re-read it I did not like it. Thank you to all who have reviewed, your comments and suggestions have been very helpful.


	3. Discovery

Chapter 2: Discovery

**Director Haversons office.**

Shinji sat in the directors office. It had been one week since he had woken up in the Infirmary. A lot had happened since then. He was still shocked about being frozen for 500 years or so, but even more so by what they had done to him. He didn't hate them for it, he knew it was that or death but the fact he had no choice in the matter rankled him. He knew this was just going to make it harder for him to fit in, to be accepted.

Shinji laughed at himself inwardly. Who was he kidding? He was never accepted any where. The only one who had every really cared for his well being was Misato, and she was dead now. Maybe things would be easier this way, he knew he was a Spartan in all but training now. Maybe if went all the way through with it, he would die and be forever at peace. Shinji hated his life, hated killing, and most of all hated himself. He wanted to die but was to much of a coward to end his own. Asuka was right about him he had no spine.

Director Haverson looked him over. He could tell the young man in front of him had a death wish, had no self esteem, and hated everything about himself. ' That will soon change, you have no idea what you're about to begin.' Haverson thought to himself.

" So shinji I wanted to talk to you about your future with us." said Haverson.

"I understand." He said.

" Seeing as you're a SPARTAN now, we're going to have to train you."

The young boy nodded. Haverson looked him over and decided that he needed to break his depression. Haverson knew how the boy felt. Having grown up in an orphanage when his mother had been killed during the covenant assault on harvest, and his father being a Marine corps Captain on the front lines. He knew neglect when he saw it. But where he had been strong, this boy had been week. He needed him strong.

" You will be leaving at 0800 tommarow morning to begin your training at Camp victory. Your Guardian will be Matthew Garmin. This means that you will be satying with him during your training."

Shinji nodded again. ' I wonder what stating with Garmin will be like.' He thought. Haverson didn't really want to waste a SPARTAN on watching him, but he was worried that in the boys current state he would attempt suicide. The UNSC needed al the SPARTANS it could get.

" Do you have any questions Shinji?"

Shinji in fact did have one " How old is Colonel Garmin? He looks young to be a colonel." he asked

" Garmin," responded Haverson " Is physically only one year older than your self. This is due to the amount of time he has spent in cryogenic stasis and in slip space. Time freezes in that enviroment. His actual age is 49 years earth standard."

Shinji nodded, this was gonna take some getting use to.

" You may go. Ill see you around." he said

Shinji left his office. It would be a while before he actually saw him.

**Six years later. Training graduation ceremony.**

Shinji walked crisply toward Colonel Garmin. A lot had happened to him in the six years since he had re-awakened. Shinji was no longer the same Spineless, cowardly boy he had once been, he was a confident young man of about 20 and the top graduate of his class. He was now an elite member of one of the toughest outfits in the UNSC. Today he was a Spartan.

He walked up to Colonel Garmin. In his time staying with him, he had come to consider him to be his brother, and he knew that Garmin looked at him like a brother also. He could see the look of pride on his brother's face.

" Congradulations graduate." Said Garmin.

He opened a small velvet box and pulled out a set of Captains bars and pinned them on Shinji's chest. He smiled at him.

" Welcome to the Spartans Captian Ikari S-513." Garmin, in an unusual display of emotion, hugged his brother for a moment. Letting him go, snapped to attention and saluted him. Shinji did the same. After the salute the crowd broke into applause. Garmin leaned over and whispered in his ear.

" I'm proud of you brother. By the way, you've been assigned to my unit. Get some rest tonight, you'll need to report aboard the UNSC Super Carrier Alexandria Tommarow at 0630 hours."

"Yes sir." Shinji said.

**One week later: Aboard Alexandria.**

Garmin stood in the briefing room, looking at his team, and its newest member.

He was immensely proud of them and glad to be finally getting some action. It was a investigative assignment true, but you never know what you going to find. On the holo-table in front of him floated the image of a large underground cavern with a run down building in it. The ruins had been discovered under Tokyo 5 by a regular sensor sweep made by the UNSC Prowler ship Artemis.

" These ruins were discovered a week ago by the Artemis. ONI wants us to go in and investigate. They believe this to be an old pre- world war three base. It is also suggested to be the command center of an organization formly know as NERV. Our job is to get inside that base and see what we can find. Captain, you will have the point on this OP."

" Yes sir." said Shinji.

" All right, get you gear on. We leave in twenty."

**Enroute to base.**

Shinji and the others checked and double checked their weapons as the Pelican neared its destination. Shinji was armed with the new MA5Z Assault rifle and the new M3S Shotgun. The rest of the unit was similarily armed except for the team sniper Gary S-486. He had favored the DMR and the Savage MA2A .50 Sniper rifle. Shinji looked down at his MOLJNER Assault armor. It was the Mark VIII, the latest version. It included a full read out of his health and the rest of the team along with a stonger energy shield and Thermal imagery capabilitys.

As they neared their entry point they saw two Wart Hog transports awaiting them. The pelican couldn't get them any closer to the access point, once they were on the ground, they would be proceeding via Wart Hog to the main entrance of the base. Once in, they go it on foot. The pelican landed dropping the ramp, and all six Spartans exited the pelican and mounted the Hogs.

" Gary you'll be driving the second Hog. I want Tom and Randy on gunner. Shinji will ride with me, Katie will ride with Gary." Colonel Garmin ordered. The Spartans all blinked green affirmation lights. With each team loaded into the Hogs, they moved up the entrance and drove down to the main doors inside the Geo- Front.

" All right everyone check your weapons. Shinji your on point from here on out."

Shinji took a clip of .45 caliber Shredder rounds and loaded them into his MA5Z.

He moved up to the heavy blast doors and hit the control panel. The doors slid open and he entered the room. As soon as he entered, he realized something was wrong. The light were on. Then a plasma burst slammed into the wall behind him. Shinji dove behind a fallen column.

" I've been engaged! Covenant hostiles!" he yelled into his mike. Immeadatly the rest of the squad came in guns blazing. It was a small group of grunts with an elite commander. As Shinji's team mates entered three grunts went down from shredder rounds, their blue blood painting the floor and walls. Then things really went to shit in Shinji's opinion. The Colonel was pinned down with his other team mates and shinji was stuck behind the fallen column, when two more elites appeared out of their Camo.

One of the elites appeared 10 feet away from Randy. The elite charges Randy with its sword drawn, as the shredder rounds from Randy's MA5Z bounce off the elites shield. He tried to roll out of the way but was too late, the elite ran his sword through his chest and out through his back. Randy's vital signs went flat as the elite kicked his limp body off the sword.

The eilite was the only one left now, the other two had disappeared down the elevator shaft after killing Randy. His energy sword was out and ready. Tom charged the Elite and was quickly slashed across the chest and smacked into the wall. He vitals now dangerously low. Shinji ran to help his team mate. When he got to Tom, he sighed in relief. The damage wasn't serious, he'd live. Shinji looked over and saw the Colonel fighting the Elite now, desperately dodging the deadly blade. The Elite kicked Garmin in the chest and slid his rifle away. Shinji ran at the Elite as it prepared to stab the Colonel. Jumping on its back he rammed the combat knife he had drawn from its sheath on his chest armor through its neck and drew his shot gun as he jumped off.. The Elite spun around pulling the knife out of its neck, to see Shinji pointing his shot gun at it.

" Die you ugly Son of a Bitch." Shinji said before pulling the trigger and blowing the Elites chest cavity against the far wall. " Don't get up." he said.

Shinji reached down and pulled the Colonel to his feet.

" Randy is dead and Toms hurt pretty bad." Shinji reported to Garmin.

" Shit. Katie radio for a medic team. Shinji and I will proceed into the base and kill those two elites." Katie blinked a green affirmative light.

Garmin looked over at Shinji and nodded. Weapons at ready, the headed through the door to a deactivated escalator. The two continued on in silence, moving down the escalator to the main floor. Garmin saw the elevators and pressed the down door to his right opened. Garmin took one look at the panel and knew it was useless, only one buuton was still operational, so he pressed it. After a minute or so the elevator stopped and the door opened to a pitch black room. Shinji had a feeling he had been here before.

" I cant see a thing, put you helmet light on." Both Garmin and Shinji turned on their helmet flood lights.

" HOLY SHIT!" Yelled Garmin. Shinji looked over at the Colonel and understood. The four green menacing eyes of unit-2 looked back at them. Shinji was confused, the last he'd seen unit-2, it had been completely destroyed by the MP EVA series and was pretty sure the pilot had been killed.

" What the hell is going on here?" he muttered to himself. He looked more to left and saw the familiar sight of Unit-00, also completely repaired. This really wasn't making sense to him. Why repair them? There wasn't any more need for the Evangelions. And if they were repaired, why weren't they used during the third world war? There actually were no mentions of these or angels, or even NERV in all the history texts he'd read in the military school on Reach.

" Sir," Shinji started " something about this doesn't feel right. I know that red EVA was destroyed, and that The one on the left of it was badly damaged."

" What are you saying captain?"

" I'm saying someone repaired them. And if they were repaired, then the pilots must also have been alive. Each Eva would only synch with one pilot, and one pilot only. Any one else whom tried to pilot them, would have a low synch ratio with it, making it impossible for it to move." Shinji stated.

" The other thing that bothers me is that in all our history books, nothing is mentioned of this. No one believed that this place even existed except me. This smells like a cover up." He finisheg

Garmin looked at him, " I agree."

The two left the room and continued their decent into the base. They had yet to see the two elites that escaped earlier and were keeping a sharp eye out for them. Shinji walked up to a door with a sign above it. The sign was now unreadable but Shinji could make out the first word.

" Cryo…" He mused.

" Captain, you find something?" Asked Garmin

" Maybe, only one way to find out." Shinji opened the door and walked in.

" Sweet Jesus." he breathed. The room was full of cryo pods filled with LCL. Their were at least twenty pods in the room. Shinji walked over to one and wiped the ice off glass plate on the front. What he saw shocked him beyond belief. Inside the pod was a blue haired girl of about twenty. Shinji couldn't mistake that face anywhere. It was Rei, Shinji went on the next and found Misato, the next one held Asuka.

" What in the hell?" he said. The colonel nodded, that's when Shinji noticed the slight Shimmer.

" SHIT! Get down!" he yelled, shoving the Colonel out of the way elites blade, only to have go through his shoulder.

" AAAGHH!" Shinji roared, as he unsheathed his combat knife and rammed it with so much force it went through the elites shield and helmet directly into its skull, killing it instantly. Shinji removed the knife with a sickening blood spray. Then turned, the other elite was there and had knocked the Colonel out. The elite had a man thrown over its shoulder. Shinji went for his gun, but the elite was to quick. Drawing its sword it slashed him across his chest and tossed him against the wall and left.

Shinji tried to sit up, but the pain was to much. So he blacked out instead.

_**A/N: Whew, that was a long one. I hope I got the battle sequences to your liking. As some may notice the armor and elites fighting style are heavily based off Halo: Reach. To those who may be picky with detail and Shinji's new, more bad ass character, let me first say that during his training, he changed a lot. I have several friend in the military, and I know that they tear you down and build you back up the way they want you. Secondly, the weaponry and ship to ship warfare weapons have greatly advanced in the now 12 years since the end of the war. Just bear that in mind, it will be important later. I hope you like the redone chapter.**_


	4. Revalations

**A/N: please re-read chapter 1-2 as they have been re-written. Thank you.**

**Aboard UNSC medical ship Merciful**.

Shinji woke up to the soft beeping of a heart monitor and a white walled room. He tried to move, but his shoulder burned like it was on fire. The memories of his last engagement came back to him, the fight in the main lobby of NERV, the fight in the cryo lab and his getting stabbed. Shinji groaned, no wonder his shoulder hurt. That Elite had stabbed him with its energy sword.

" Damn it." he muttered, knowing this was going to remove him from duty for a time. Shinji heard a faint rustling near by and looked over at the other bed in the room to see a girl with blue hair on the bed next to him. Shinji started, thinking she was awake, but realized quickly she was still asleep as he heard her even breathing and rhythmic rise and fall of her chest. Shinji breathed a sigh of relief, he really didn't feel like explaining the situation to her right now. Better leave that to Section three. Shinji heard the door hiss and looked over to see Matt walk in.

" How's your shoulder, Captain?"

" Hurts Colonel." Shinji responded. " I'm assuming that, since Rei is here, the other that were in Cryo stasis have also been successfully revived?" He asked.

"Yes that have. All except one, which is what I'm here to talk to you about. We need to discuss one Gendo Ikari."

" Ok Sir, shouldn't we go to your office?" Shinji asked pointedly, while glancing at Rei. Garmin Caught the look and the meaning behind it.

" Its fine, she wont wake up yet. She's still…Recovering."

" Recovering?" He asked. " From what, being frozen for five hundred years?"

" Um, not exactly, she kind of sedated. We'll discuss that later Captain."

Shinji had an idea of what had transpired, but he would wait until the Colonel would tell him.

" So what about My father?" He asked.

Garmin looked surprised. This was something that Shinji hadn't mentioned before. He wondered why he never spoke about his father before. Garmin was kind of jealous, he had never met his father, and never would. His father had died during the engagement on Harvest.

" So that man was your Father?" He asked.

" Yes, that Bastard was my father."

" Well the Elites have that bastard, as you put it, and that isn't something ONI and the UNSC can allow."

" What do you mean?"

" Your father knows all the information regarding the original Evangelion project. We have reason to believe that your father was their intended target. It is also ONI's belief that, with him, the Covenant will try to launch their own Evangelion project."

" What do you mean original?"

" The UNSC has launched their own Evangelion Project. We have Six completed Eva's along with unit 01 and now units 00 and 02."

" Oh." Said Shinji. He cursed himself for thinking that ONI wouldn't attempt to construct Evangelions. They were a very effective weapon after all, and with concerns growing over the increase in Covenant activity recently, the UNSC would want any weapon that could give them the means to keep the Covenant at bay. Still, he didn't like the idea of more Evangelions, more lives ruined.

As if reading his thoughts, Garmin said " And with the recent increase in Covenant activity, the UNSC and ONI are getting a little fidgety. And the ongoing civil war on Sanghelios isn't helping things any. The Elites have been our allies since the end of the war. Well, at least those that don't believe in the Great Journey. But a small sect of the Sangheli still believe, and the UNSC believes that they may have joined ranks with the Covenant."

Shinji nodded as he listened. Now knowing the full extent of the problem, and the impending threat of another war with the Covenant, one that could possibly involve Eva's, he knew what needed to be done.

" We need to find my father. He is the key to this. If we can get him back, before the Covenant attain Eva's, maybe we can avert war, or at least minimize it."

" Agreed."

"Now, what about Rei? You said she was recovering, she isn't like… like us is she?" he asked.

Garmin sighed and began to explain the course of events that lead up to this. Shinji listened as Garmin recounted how, after being stabbed the Elite had turned back and Went for Rei's pod. Garmin tried to stop him, but wasn't fast enough to stop him. The Elite stabbed Rei. With no other options available, Garmin and Halsey, along with Director Haverson decided that the only way to save her life was to undergo augmentation. " She barley survived it." Garmin finished.

" The stabbing, or the augmentation?"

" Both."

" What about training?"

" She already has an extensive background in combat. Trained as an Eva pilot and receiving basic combat training since she was about 8, according to records we've recovered, it should only take her maybe 3 to 4 month to be up to speed with the rest of us."

Shinji thought about that. He admitted that he hadn't really known her to well back on earth, but he never assumed her actual training was close to that of his own. As he looked over to her, he felt a strange sensation in his stomach. He couldn't really figure out what it was, and after a few minutes of contemplating it, he pushed aside. He had no time for emotions right now. They could wait.

Garmin was getting ready to leave. He in informed Shinji that he would be leaving the hospital in a little over a week, he had nerve damage in his shoulder from the plasma the sword emitted, and the doctors wanted to ensure a full recovery. As he left he told Shinji to get some rest. To which Shinji responded with a smile, " I'll sleep when I'm dead, Sir." Garmin smiled.

" Like wise Captain."

Garmin left, leaving Shinji alone with his thoughts. Shinji again looked over to the sleeping form of the blue haired girl, wondering when she'd wake up. He felt that strange feeling again in his stomach. He couldn't tell what is was and was slightly concerned by it. Well, he thought dryly, 'I have nothing but time.' As he pondered the sensation, he briefly wondered where Asuka and others were. " Well," he muttered, " I suppose I'll find out soon enough."

Shinji noticed that he was beginning to feel drowsy. He took more look over to Rei and said a silent prayer for her safe recovery, then fell asleep.

**A/N: Sorry this chapter wasn't as long as the last two, but I wanted save further introductions for the next chapter as that would make this one really long. I hope you liked this and thank you every one who reviewed the first two chapters, your comments and advice really helped me a lot. As always read and review! ****J**


	5. Old Friends, New Unit

_**Chapter 4**_

_**Dr. Ritsuko Akagi sat in a non descript exam room, ogling all the electronics in the room. To say she was in heaven was an understatement. She wished she had time to look at them before Dr. Halsey came back. After about 10 minutes of waiting, she got up and began to examine a set of controls on the wall. She was still looking the control panel over when Halsey walked in.**_

" _**Well looks like… umm, why are looking at the door control panel?" Halsey asked.**_

" _**Oh!" Ritsuko exclaimed, " I'm so sorry, this is a door control?" She asked. Inwardly she cursed herself. Of course this was door control panel, it was right next to the door. **_

" _**Yes, it is. Any way, you checked out ok, no health issues or negative side effects from the prolonged Cryo Stasis. Your free to go." Halsey said.**_

_**Ritsuko nodded and thanked the Doctor. Outside the room she ran in to Misato Katsuragi. She was wearing a military fatigues, same as Ritsuko was. The UNSC had taken their old clothing and discarded it for fear of contamination. **_

" _**Hey Ritz, they let you out to?" she asked happy to see her friend again.**_

" _**Yes they did. What do you think of all this?" She asked, gesturing all around her.**_

" _**I don't know, I cant understand half of what the people are saying around here." She complained. Misato hated not understanding what people were saying, almost as much as she hated not having beer on hand. **_

" _**Well, I'd love to get a chance to look at all the tech they have, its fascinating."**_

_**Misato was about to reply when a tall man in his twenties came around the corner flanked by Toji, Asuka, Hikari, and Kensuke. He looked at the two women and smiled.**_

" _**Misato Katsuragi and Ritsuko Akagi?" he asked. Both women nodded, stunned at his impressive size and bearing. While he seemed friendly, he spoke with an air of authority and had a spine of steel. **_

" _**If you'll follow me, there is some one who wants to see you all." **_

_**He led them down the corridor to a recovery room. **_

" _**Hey Captain, you have some visitors." **_

_**The man on the hospital bed looked up from the food he had been eating. What ever it was, it didn't look edible. The man stepped aside and allowed the six them in the room. When he came into view, every one gasped. On the bed before them sat Shinji Ikari, though not as they remembered him. He was as tall as the man who had led them here, and a lot stronger by the look of him. He also, even lying in a hospital bed, had a air of confidence and authority about him. **_

" _**Thank you Colonel." Shinji said.**_

" _**Hey, you don't have to call me Colonel, Shinj, you're off duty and were brothers." Colonel Garmin said.**_

" _**Okay, Matt, fine. So this is every one?" He said looking over and waving to the assembled group, who was still getting over the shock of seeing him alive. **_

" _**Yes. I heard the doctor is planning on releasing you later today. Rei as well, seeing as her Augmentation was successfully completed." Garmin said. The assembled group looked at Garmin. He knew where Rei was? No one had seen her since their rescue and her being put on the medi-vac Pelican. Ritsuko was curious, what was Augmentation?**_

" _**Good, that means I can get back to active duty. I hate hospitals, freakin boring as all hell in here." Shinji said. Garmin nodded, he to hated hospitals. In fact most Spartans hated hospitals. Usually ending up there meant you screwed up somehow. **_

_**Garmin was about to say something when a voice came over the PA.**_

" _**Colonel Garmin, please report to Director Haverson's office. I repeat would Colonel Garmin report to Director Haverson's Office." **_

" _**Ah Crap, well looks like I got to go. Ill see you later Shinji. Hopefully I'm not getting sent on a suicide mission…Again." Garmin joked. **_

" _**Yea me to." Shinji said to him as he left. Shinji then turned his attention to his visitors. He thought he would be happy to see them, and he was, but it felt off. He didn't feel like he related to them any more. It was strange, he interacted well with the other Spartans, but these people he'd know and fought next to, felt like strangers. Have I changed that much? He asked himself. Finally, deciding it would be better to say something than sit there looking like moron he said**_

" _**Hello…. How is everyone?" **_

_**He winced inwardly, after not seeing each other for 500 years, that's the best he can do? How ever, it was enough to break the ice, next thing he knew, he was being strangled by Misato as she hugged him. **_

" _**Misato, cant breath!" he said through choked breaths. He'd forgotten how well hard she used to hug to people. **_

" _**Oh my God! I cant believe you're alive! This is a miracle!" She exclaimed while sobbing into his shoulder. **_

" _**Back then, we thought… we thought we had lost you, for good." **_

_**Shinji was still struggling for breath when Misato's choke hold was broken by Ritsuko. **_

" _**Geez, Let the poor kid breath Misato." She said. Misato let go and apologized for her out burst. Shinji looked over to see Asuka and Toji still looking at him. He saw a flash in Asuka's eyes remembered she'd get that look just before deciding to ridicule him, or beat him. Good thing he was a lot stronger now.**_

" _**So, you're alive Third? " She asked Contempt in her voice.**_

" _**No, your just imagining this. Obviously I'm alive." he said sarcastically. He really wasn't in a mood to deal with her crap. Again every one was shocked, Shinji normally would have cowered before her, instead he talked back. She was struck dumb by his talk. . She couldn't respond.**_

" _**Asuka? You ok? You look like you've seen a ghost." Shinji asked her. Asuka got up and ran from the room, leaving everyone stunned, including the blue haired girl who just entered the room. **_

" _**What got into her?" Rei asked**_

_**Shinji looked at her and felt that familiar sensation**_

" _**Beats the hell out of me." Every one else nodded, confused as he was.**_

_**Director Haverson's Office.**_

_Garmin sat in the Directors office reading over series of files that had been handed to him. The files all regarded ONI's own Evangelion project and it completion. Currently he was looking at updates on the refit and repair of units 00 and 02. He also had a list of potential pilots in front of him. _

" _So these are the pilots?" he asked, most of them were Spartans, except for the two pilots Sohryu and Suzahara. He wasn't surprised by the choice of those two as pilots. He had read the Nerv reports and knew Toji had once been a pilot. They had even found a partially rebuilt Unit 03 in the old Nerv head quarters. _

" _Yes, they are. They will all be briefed on their new assignments tomorrow morning. You will deliver the briefing, as you are their new Commanding Officer."_

" _I understand sir." _

" _Good. Captain Ikari will handle their training, seeing as he has experience with this." _

" _Understood sir. Sir? Do we have any leads on the where abouts of Gendo Ikari?"_

" _No, but you'll be the first to know if we do. While finding him is priority, getting our Eva's up and running is top. We need them if the Covenant are going hit us again. Especially if they to have Eva's." _

" _Yes sir I understand. Sir what about the elites that captured him? I thought they were on our side?"_

" _They are Colonel, but, the Sangheli are in the middle of a civil war. Some side with the prophets, others with the arbiter. I'm afraid we cant count on their help with this one."_

_Garmin nodded, it made sense. a lot of things had changed since the wars end. Many of the Elites hadn't approved of the schism when it had originally happened. The only reason so many had gone along with it in the beginning was because of the flood threat. Haverson's phone rang._

" _Yes, this is Haverson. I understand, thank you."_

" _Looks like you're gonna meet your new unit sooner than I thought."_

" _Sir?" _

" _We lost contact with our research facility on Solaris Prime. I'm sending your new squad to investigate."_

" _Sir what about the two non Spartans and Rei? They aren't trained."_

_The director thought about it. " Your concern is noted Colonel, Sohryu and Suzahara will remain here and begin training under CPO Klienman. Rei will go with you, she has enough experience."_

" _Understood sir."_

" _Good. Assemble your team. Wheels up in twenty."_

_A/N: Gotta love a good Cliff hangar! __J till next time! Please read and review!_


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